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		<title>Identification - Spectral DB search</title>
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<h1>Spectral DB search</h1>

<h2>Description</h2>
<p>
Run on any feature list to match all rows against a local spectral library (formats: MoNA json, NIST msp, GNPS json (internal library submission format), JCAMP-DX jdx).
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<h4>Method parameters</h4>
<dl>
<dt>Peaklist</dt>
	<dd>Select any peaklist</dd>
<dt>Masslist</dt>
	<dd>Masslist of scans</dd>
<dt>Spectral database file</dt>
	<dd>json/msp from MoNA (MassBank of North America)</dd>
	<dd>msp NIST format</dd>
	<dd>JCAMP-DX jdx</dd>
	<dd>mgf format from GNPS</dd>
<dd>json GNPS (format from the spectral DB submission module)</dd>
	<dt>MS level</dt>
	<dd>Set MS level to "1" to compare MS1 spectra (e.g. GC-EI-MS data) or set it to "2" or higher for MS/MS scans</dd>
<dt>Precursor m/z tolerance </dt>
	<dd>Only used for MS level > 1. Filter all library entries by precursor m/z. </dd>	
<dt>13C deisotoping </dt>
	<dd>Deletes 13C isotope signals in the query and library mass spectra</dd>	
	<dd>Monotonic shape: Especially, for small molecules. 13C isotope pattern with first signal as the most abundant</dd>	
<dt>Min matched isotope signals</dt>
	<dd>Minimum number of "isotope" signals that need to be matched in the query and library scan. Searches for putative: </dd>
	<dd>13C signals </dd>
	<dd>-H (M+ to M+H+) and -2H signals </dd>
	<dd>Cl isotope signals </dd>
<dt>Crop spectra to m/z overlap </dt>
	<dd>Only match signals that fall within the overlapping m/z range of both spectra (bounds are expanded by spectral m/z tolerance))</dd>	
<dt>Spectral m/z tolerance </dt>
	<dd>Tolerance to match signals in the two spectra (library and query) </dd>	
<dt>Retention time tolerance</dt>
	<dd>Optional: Only used if the DB entry has a retention time</dd>
<dt>Noise level</dt>
	<dd>An additional noise level for masslists (masslists are typically already thresholded)</dd>
<dt>Minimum matched signals</dt>
	<dd>Minimum number of signals within m/z tolerance in a masslist and the spectral library entry</dd>
<dt>Similarity</dt>
	<dd>Different similarity functions to match query and library spectra</dd>
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